MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : forcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3553 b3399 b4382 b1241 b0351 b4069 b2502 b2744 b3708 b3115 b1849 b2296 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b3449 b1033 b0675 b2361 b0261 b4381 b2406 b0112 b0114 b0509 b3125 b1539 b2492 b0904 b1533 b0494   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.513231 (mmol/gDw/h)
  Minimum Production Rate : 0.502974 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.098606
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.077669
  EX_pi_e : 2.003988
  EX_so4_e : 0.632216
  EX_k_e : 0.100179
  EX_fe2_e : 0.008243
  EX_mg2_e : 0.004452
  EX_ca2_e : 0.002671
  EX_cl_e : 0.002671
  EX_cu2_e : 0.000364
  EX_mn2_e : 0.000355
  EX_zn2_e : 0.000175
  EX_ni2_e : 0.000166
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.064765
  EX_co2_e : 21.424275
  EX_h_e : 9.460389
  EX_ac_e : 3.207350
  Auxiliary production reaction : 0.502974
  DM_oxam_c : 0.014003
  DM_5drib_c : 0.000344
  EX_glyclt_e : 0.000343
  DM_4crsol_c : 0.000114

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

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Last updated: 21-Sep-2023
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